Award-winning director Michael Moore's film, Fahrenheit 911, criticises Bush policies before the 11 September 2001 attacks on the United States.
The film also alleges financial connections between the Bush family, its associates and prominent Saudi Arabian families, including that of Usama bin Ladin.
Disney head Michael Eisner told US media network CNBC on Wednesday that Fahrenheit 911 "is a totally appropriate film ... but we did not want to have it in the middle of a political process. We are a non-partisan company."
An entry at this month's Cannes Film Festival, the documentary closely explores the US government's role in the evacuation of bin Ladin relatives from the United States after the September 11 attacks.
Moore describes the film as a "comedy."
Disney has a contractual agreement with Miramax bosses Bob and Harvey Weinstein to prevent Miramax from distributing films under certain circumstances, including having an excessive budget or an NC-17 rating which precludes viewing by minors.
But executives at Miramax believe Disney's ban on Moore's documentary falls outside the scope of the agreement and say they may seek mediation on the issue, people involved in the production of the film told the New York Times.
Miramax, which Disney bought 10 years ago, became a principal investor in Moore's project a year ago. But Disney spokeswoman Zenia Mucha said Disney would not budge from its position.
The mouse that roared 'No' says
it wants to remain non-partisan
The ban if enforced would block the distribution of Fahrenheit 911 in North America but overseas rights have been sold to a number of companies, Disney executives said.
Moore won a special Cannes prize two years ago for Bowling for Columbine, which went on to win an Oscar. He took advantage of the film's presentation at Cannes in 2002 to attack Bush's policies.